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        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in multiqc_data when this report was generated.


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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        Tool Citations

        Please remember to cite the tools that you use in your analysis.

        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.26

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        This report has been generated by the nf-core/quantms analysis pipeline. For information about how to interpret these results, please see the documentation.

        Report generated on 2025-04-07, 07:28 UTC based on data in: /home/runner/work/pmultiqc/pmultiqc/data


        pmultiqc

        pmultiqc is a MultiQC module to show the pipeline performance of mass spectrometry based quantification pipelines such as nf-core/quantms, MaxQuant.URL: https://github.com/bigbio/pmultiqc

        Experimental Design

        This table shows the design of the experiment. I.e., which files and channels correspond to which sample/condition/fraction.

        You can see details about it in https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/classOpenMS_1_1ExperimentalDesign.html

        Showing 0/4 rows and 6/6 columns.
        Spectra FileFraction_GroupFractionLabelSampleMSstats_ConditionMSstats_BioReplicate
        20200103_HepG2_sp3_TMT_BP123_F1
        1
        1
        1|2|3|4|5|6
        1|2|3|4|5|6
        ControlControlControlBaPBaPBaP
        1|2|3|4|5|6
        20200103_HepG2_sp3_TMT_BP123_F2
        1
        2
        1|2|3|4|5|6
        1|2|3|4|5|6
        ControlControlControlBaPBaPBaP
        1|2|3|4|5|6
        20200103_HepG2_sp3_TMT_BP456_F1
        2
        1
        1|2|3|4|5|6
        7|8|9|10|11|12
        ControlControlControlBaPBaPBaP
        7|8|9|10|11|12
        20200103_HepG2_sp3_TMT_BP456_F2
        2
        2
        1|2|3|4|5|6
        7|8|9|10|11|12
        ControlControlControlBaPBaPBaP
        7|8|9|10|11|12

        HeatMap

        This heatmap shows a performance overview of the pipeline

        This plot shows the pipeline performance overview. Some metrics are calculated.

        • Heatmap score[Contaminants]: as fraction of summed intensity with 0 = sample full of contaminants; 1 = no contaminants
        • Heatmap score[Pep Intensity (>23.0)]: Linear scale of the median intensity reaching the threshold, i.e. reaching 2^21 of 2^23 gives score 0.25.
        • Heatmap score[Charge]: Deviation of the charge 2 proportion from a representative Raw file (median). For typtic digests, peptides of charge 2 (one N-terminal and one at tryptic C-terminal R or K residue) should be dominant. Ionization issues (voltage?), in-source fragmentation, missed cleavages and buffer irregularities can cause a shift (see Bittremieux 2017, DOI: 10.1002/mas.21544 ).
        • Heatmap score [MC]: the fraction (0% - 100%) of fully cleaved peptides per Raw file
        • Heatmap score [MC Var]: each Raw file is scored for its deviation from the ‘average’ digestion state of the current study.
        • Heatmap score [ID rate over RT]: Judge column occupancy over retention time. Ideally, the LC gradient is chosen such that the number of identifications (here, after FDR filtering) is uniform over time, to ensure consistent instrument duty cycles. Sharp peaks and uneven distribution of identifications over time indicate potential for LC gradient optimization.Scored using ‘Uniform’ scoring function. i.e. constant receives good score, extreme shapes are bad.
        • Heatmap score [MS2 Oversampling]: The percentage of non-oversampled 3D-peaks. An oversampled 3D-peak is defined as a peak whose peptide ion (same sequence and same charge state) was identified by at least two distinct MS2 spectra in the same Raw file. For high complexity samples, oversampling of individual 3D-peaks automatically leads to undersampling or even omission of other 3D-peaks, reducing the number of identified peptides.
        • Heatmap score [Pep Missing]: Linear scale of the fraction of missing peptides.
        Created with MultiQC

        Summary Table

        This table shows the quantms pipeline summary statistics

        This table shows the quantms pipeline summary statistics

        Showing 0/1 rows and 5/5 columns.
        #MS2 Spectra#Identified MS2 Spectra%Identified MS2 Spectra#Peptides Identified#Proteins Identified#Proteins Quantified
        165009
        98329
        59.59%
        34585
        4073
        4073

        Pipeline Result Statistics

        This plot shows the quantms pipeline final result

        This plot shows the quantms pipeline final result. Including Sample Name、Possible Study Variables、identified the number of peptide in the pipeline、 and identified the number of modified peptide in the pipeline, eg. All data in this table are obtained from the out_msstats file. You can also remove the decoy with the remove_decoy parameter.

        Showing 0/4 rows and 7/7 columns.
        Spectra FileSample NameConditionFraction#Peptide IDs#Unambiguous Peptide IDs#Modified Peptide IDs#Protein (group) IDs
        20200103_HepG2_sp3_TMT_BP123_F1
        1|2|3|4|5|6
        ControlControlControlBaPBaPBaP
        1
        19223
        7746
        19223
        5365
        20200103_HepG2_sp3_TMT_BP123_F2
        1|2|3|4|5|6
        ControlControlControlBaPBaPBaP
        2
        16794
        6781
        16794
        5196
        20200103_HepG2_sp3_TMT_BP456_F1
        7|8|9|10|11|12
        ControlControlControlBaPBaPBaP
        1
        19442
        7778
        19442
        5513
        20200103_HepG2_sp3_TMT_BP456_F2
        7|8|9|10|11|12
        ControlControlControlBaPBaPBaP
        2
        17424
        6994
        17424
        5261

        Number of Peptides identified Per Protein

        This plot shows the number of peptides per protein in quantms pipeline final result

        This statistic is extracted from the out_msstats file. Proteins supported by more peptide identifications can constitute more confident results.

        Created with MultiQC

        Spectra Tracking

        This plot shows the tracking of the number of spectra along the quantms pipeline

        This table shows the changes in the number of spectra corresponding to each input file during the pipeline operation. And the number of peptides finally identified and quantified is obtained from the PSM table in the mzTab file. You can also remove decoys with the remove_decoy parameter.:

        • MS1_Num: The number of MS1 spectra extracted from mzMLs
        • MS2_Num: The number of MS2 spectra extracted from mzMLs
        • MSGF: The Number of spectra identified by MSGF search engine
        • Comet: The Number of spectra identified by Comet search engine
        • Sage: The Number of spectra identified by Sage search engine
        • PSMs from quant. peptides: extracted from PSM table in mzTab file
        • Peptides quantified: extracted from PSM table in mzTab file
        Showing 0/4 rows and 6/6 columns.
        Spectra File#MS1 Spectra#MS2 SpectraMSGFComet#PSMs from quant. peptides#Peptides quantified
        20200103_HepG2_sp3_TMT_BP123_F1
        12817
        41175
        32418
        32416
        25913
        19179
        20200103_HepG2_sp3_TMT_BP123_F2
        12454
        41511
        30781
        30282
        22762
        16711
        20200103_HepG2_sp3_TMT_BP456_F1
        12916
        41008
        32181
        32242
        25894
        19399
        20200103_HepG2_sp3_TMT_BP456_F2
        12654
        41315
        31650
        30994
        23760
        17330

        Summary of Search Engine Scores

        These plots contain search scores and PEPs counts for different search engines in different files, and they also contain a summary of the consensus PSMs if two or more search engines are used

        This statistic is extracted from idXML files.


        SpecEvalue Description

                    SpecEvalue : Spectral E-values, the search score of MSGF. The value used for plotting is -lg(SpecEvalue).
        
        Created with MultiQC

        xcorr description

                    xcorr : cross-correlation scores, the search score of Comet. The value used for plotting is xcorr.
        
        Created with MultiQC

        Summary of Posterior Error Probabilities (PEP)

        Created with MultiQC

        Summary of consensus PSMs

                    No Consensus PSMs data because of single search engine!
        

        Distribution of precursor charges

        This is a bar chart representing the distribution of the precursor ion charges for a given whole experiment.

        This information can be used to identify potential ionization problems including many 1+ charges from an ESI ionization source or an unexpected distribution of charges. MALDI experiments are expected to contain almost exclusively 1+ charged ions. An unexpected charge distribution may furthermore be caused by specific search engine parameter settings such as limiting the search to specific ion charges.

        Created with MultiQC

        Number of Peaks per MS/MS spectrum

        This chart represents a histogram containing the number of peaks per MS/MS spectrum in a given experiment. This chart assumes centroid data. Too few peaks can identify poor fragmentation or a detector fault, as opposed to a large number of peaks representing very noisy spectra. This chart is extensively dependent on the pre-processing steps performed to the spectra (centroiding, deconvolution, peak picking approach, etc).

        Created with MultiQC

        Peak Intensity Distribution

        This is a histogram representing the ion intensity vs. the frequency for all MS2 spectra in a whole given experiment. It is possible to filter the information for all, identified and unidentified spectra. This plot can give a general estimation of the noise level of the spectra.

        Generally, one should expect to have a high number of low intensity noise peaks with a low number of high intensity signal peaks. A disproportionate number of high signal peaks may indicate heavy spectrum pre-filtering or potential experimental problems. In the case of data reuse this plot can be useful in identifying the requirement for pre-processing of the spectra prior to any downstream analysis. The quality of the identifications is not linked to this data as most search engines perform internal spectrum pre-processing before matching the spectra. Thus, the spectra reported are not necessarily pre-processed since the search engine may have applied the pre-processing step internally. This pre-processing is not necessarily reported in the experimental metadata.

        Created with MultiQC

        Oversampling Distribution

        An oversampled 3D-peak is defined as a peak whose peptide ion (same sequence and same charge state) was identified by at least two distinct MS2 spectra in the same Raw file.

        For high complexity samples, oversampling of individual 3D-peaks automatically leads to undersampling or even omission of other 3D-peaks, reducing the number of identified peptides. Oversampling occurs in low-complexity samples or long LC gradients, as well as undersized dynamic exclusion windows for data independent acquisitions.

                    * Heatmap score [EVD: MS2 Oversampling]: The percentage of non-oversampled 3D-peaks.
        
        Created with MultiQC

        Delta Mass

        This chart represents the distribution of the relative frequency of experimental precursor ion mass (m/z) - theoretical precursor ion mass (m/z).

        Mass deltas close to zero reflect more accurate identifications and also that the reporting of the amino acid modifications and charges have been done accurately. This plot can highlight systematic bias if not centered on zero. Other distributions can reflect modifications not being reported properly. Also it is easy to see the different between the target and the decoys identifications.

        Created with MultiQC

        Peptides Quantification Table

        This plot shows the quantification information of peptides in the final result (mainly the mzTab file).

        The quantification information of peptides is obtained from the MSstats input file. The table shows the quantitative level and distribution of peptides in different study variables, run and peptiforms. The distribution show all the intensity values in a bar plot above and below the average intensity for all the fractions, runs and peptiforms.

        • BestSearchScore: It is equal to 1 - min(Q.Value) for DIA datasets. Then it is equal to 1 - min(best_search_engine_score[1]), which is from best_search_engine_score[1] column in mzTab peptide table for DDA datasets.
        • Average Intensity: Average intensity of each peptide sequence across all conditions with NA=0 or NA ignored.
        • Peptide intensity in each condition (Eg. CT=Mixture;CN=UPS1;QY=0.1fmol): Summarize intensity of fractions, and then mean intensity in technical replicates/biological replicates separately. Click Show replicates to switch to bar plots for every replicate.
        Showing 0/50 rows and 6/6 columns.
        PeptideIDProtein NamePeptide SequenceBest Search ScoreAverage IntensityControlBaP
        1
        sp|P36578|RL4_HUMAN
        AAAAAAALQAK
        1.0000
        5.2809
        5.2578
        5.3028
        2
        sp|Q9BTD8-2|RBM42_HUMAN;sp|Q9BTD8-3|RBM42_HUMAN;sp|Q9BTD8-4|RBM42_HUMAN;sp|Q9BTD8|RBM42_HUMAN
        AAAAATVVPPMVGGPPFVGPVGFGPGDR
        1.0000
        4.4763
        4.4339
        4.5149
        3
        sp|Q9P258|RCC2_HUMAN
        AAAAAWEEPSSGNGTAR
        1.0000
        4.9573
        4.9507
        4.9638
        4
        sp|Q8TCS8|PNPT1_HUMAN
        AAAAGR
        0.9988
        5.2126
        5.1736
        5.2484
        5
        sp|Q8WWH5|TRUB1_HUMAN
        AAAAVVAAAAR
        1.0000
        5.4480
        5.4245
        5.4703
        6
        sp|Q96L58|B3GT6_HUMAN
        AAAFLAVLVASAPR
        1.0000
        3.6403
        3.6670
        3.6118
        7
        sp|Q8N4T8-2|CBR4_HUMAN;sp|Q8N4T8|CBR4_HUMAN
        AAAGDLGGDHLAFSCDVAK
        1.0000
        4.9939
        4.9871
        5.0006
        8
        sp|Q8NFD5-2|ARI1B_HUMAN;sp|Q8NFD5-3|ARI1B_HUMAN;sp|Q8NFD5|ARI1B_HUMAN
        AAAGSAAGGFQR
        1.0000
        4.8020
        4.8162
        4.7874
        9
        sp|P62070-4|RRAS2_HUMAN;sp|P62070|RRAS2_HUMAN
        AAAGWR
        0.9905
        5.1278
        5.0651
        5.1827
        10
        sp|P51970|NDUA8_HUMAN
        AAAHHYGAQCDKPNK
        1.0000
        5.1076
        5.1231
        5.0914
        11
        sp|P31948-2|STIP1_HUMAN;sp|P31948|STIP1_HUMAN
        AAALEFLNR
        1.0000
        5.2624
        5.2860
        5.2375
        12
        sp|Q9NX63|MIC19_HUMAN
        AAANEQLTR
        1.0000
        5.2240
        5.2244
        5.2235
        13
        CONTAMINANT_Q0IIK2;CONTAMINANT_Q29443
        AAANFFSASCVPCADQSSFPK
        1.0000
        4.9757
        4.9912
        4.9596
        14
        sp|P53618|COPB_HUMAN
        AAAQCYIDLIIK
        1.0000
        5.0671
        5.0873
        5.0459
        15
        sp|Q92506|DHB8_HUMAN
        AAAQETVR
        1.0000
        5.1944
        5.1750
        5.2130
        16
        sp|Q9NVA2-2|SEP11_HUMAN;sp|Q9NVA2|SEP11_HUMAN
        AAAQLLQSQAQQSGAQQTK
        1.0000
        5.1698
        5.1415
        5.1963
        17
        sp|Q8TAQ2-2|SMRC2_HUMAN;sp|Q8TAQ2-3|SMRC2_HUMAN;sp|Q8TAQ2|SMRC2_HUMAN
        AAASATR
        0.9987
        5.4889
        5.4687
        5.5082
        18
        sp|P30153|2AAA_HUMAN
        AAASHK
        1.0000
        5.3727
        5.3851
        5.3600
        19
        sp|Q10570|CPSF1_HUMAN
        AAASVLTTSMVTMEPGYLFLGSR
        1.0000
        4.3477
        4.3196
        4.3741
        20
        sp|Q99733-2|NP1L4_HUMAN;sp|Q99733|NP1L4_HUMAN
        AAATAEEPDPK
        1.0000
        5.2740
        5.2408
        5.3048
        21
        sp|P14555|PA2GA_HUMAN
        AAATCFAR
        1.0000
        5.7174
        5.6998
        5.7342
        22
        sp|Q03252|LMNB2_HUMAN
        AAATMATPLPGR
        1.0000
        5.3500
        5.3130
        5.3842
        23
        sp|P19338|NUCL_HUMAN
        AAATPAK
        0.9998
        5.5584
        5.4680
        5.6332
        24
        sp|P49006|MRP_HUMAN
        AAATPESQEPQAK
        1.0000
        5.2541
        5.2176
        5.2878
        25
        sp|Q7KZF4|SND1_HUMAN
        AAATQPDAK
        1.0000
        5.2756
        5.2713
        5.2798
        26
        sp|P19338|NUCL_HUMAN
        AAATSAK
        1.0000
        5.9501
        5.8938
        5.9999
        27
        sp|P09327|VILI_HUMAN
        AAATTAQEYLK
        1.0000
        5.2115
        5.1615
        5.2564
        28
        sp|P18206-2|VINC_HUMAN;sp|P18206|VINC_HUMAN
        AAAVGTANK
        1.0000
        5.1440
        5.1509
        5.1370
        29
        sp|P19404|NDUV2_HUMAN
        AAAVLPVLDLAQR
        1.0000
        4.8615
        4.8252
        4.8950
        30
        sp|Q8N697|S15A4_HUMAN
        AACGAVLLTELLER
        1.0000
        4.3789
        4.3359
        4.4180
        31
        sp|Q9BX93-2|PG12B_HUMAN;sp|Q9BX93|PG12B_HUMAN
        AACICAEEEKEEL
        1.0000
        5.0117
        5.0061
        5.0171
        32
        sp|Q9UBQ7|GRHPR_HUMAN
        AADCEVEQWDSDEPIPAK
        1.0000
        5.6366
        5.6076
        5.6638
        33
        sp|O94855-2|SC24D_HUMAN;sp|O94855|SC24D_HUMAN
        AADCPGK
        1.0000
        5.1754
        5.1437
        5.2049
        34
        sp|O43143|DHX15_HUMAN
        AADEAK
        0.9984
        5.6558
        5.6000
        5.7051
        35
        sp|Q9Y277-2|VDAC3_HUMAN;sp|Q9Y277|VDAC3_HUMAN
        AADFQLHTHVNDGTEFGGSIYQK
        1.0000
        4.8620
        4.8470
        4.8766
        36
        sp|Q9NQX3-2|GEPH_HUMAN;sp|Q9NQX3|GEPH_HUMAN
        AADGPGDR
        1.0000
        5.0761
        5.0870
        5.0650
        37
        sp|O95782-2|AP2A1_HUMAN;sp|O95782|AP2A1_HUMAN
        AADLLYAMCDR
        1.0000
        4.3776
        4.3283
        4.4219
        38
        sp|P67809|YBOX1_HUMAN
        AADPPAENSSAPEAEQGGAE
        1.0000
        4.8359
        4.7967
        4.8718
        39
        sp|Q92805|GOGA1_HUMAN
        AADQTTAEQGMR
        1.0000
        4.9763
        4.9925
        4.9593
        40
        sp|Q1ED39|KNOP1_HUMAN
        AADSLQQNLQR
        1.0000
        4.9904
        4.9590
        5.0197
        41
        sp|P12270|TPR_HUMAN
        AADSQNSGEGNTGAAESSFSQEVSR
        1.0000
        4.7658
        4.7010
        4.8222
        42
        sp|O15400|STX7_HUMAN
        AADYQR
        0.9999
        5.0564
        5.0087
        5.0993
        43
        sp|Q9Y5U8|MPC1_HUMAN
        AADYVR
        0.9997
        5.5275
        5.5065
        5.5475
        44
        sp|Q3KQV9|UAP1L_HUMAN
        AAEACAR
        0.9997
        4.6971
        4.6674
        4.7249
        45
        sp|P55884-2|EIF3B_HUMAN;sp|P55884|EIF3B_HUMAN
        AAEAEPR
        0.9999
        5.6091
        5.5562
        5.6563
        46
        sp|Q14554|PDIA5_HUMAN
        AAEALHGEADSSGVLAAVDATVNK
        1.0000
        4.9613
        4.9965
        4.9230
        47
        sp|Q08211|DHX9_HUMAN
        AAECNIVVTQPR
        1.0000
        5.1486
        5.1244
        5.1715
        48
        sp|P14543-2|NID1_HUMAN;sp|P14543|NID1_HUMAN
        AAECVHR
        0.9998
        4.8027
        4.7709
        4.8323
        49
        sp|P06454-2|PTMA_HUMAN;sp|P06454|PTMA_HUMAN
        AAEDDEDDDVDTK
        1.0000
        6.6558
        6.6211
        6.6880
        50
        sp|P06454-2|PTMA_HUMAN;sp|P06454|PTMA_HUMAN
        AAEDDEDDDVDTKK
        1.0000
        6.3845
        6.3543
        6.4128

        Protein Quantification Table

        This plot shows the quantification information of proteins in the final result (mainly the mzTab file).

        The quantification information of proteins is obtained from the msstats input file. The table shows the quantitative level and distribution of proteins in different study variables and run.

        • Peptides_Number: The number of peptides for each protein.
        • Average Intensity: Average intensity of each protein across all conditions with NA=0 or NA ignored.
        • Protein intensity in each condition (Eg. CT=Mixture;CN=UPS1;QY=0.1fmol): Summarize intensity of peptides.

        Click Show replicates to switch to bar plots of quantities in each replicate.

        Showing 0/50 rows and 5/5 columns.
        ProteinIDProtein NameNumber of PeptidesAverage IntensityControlBaP
        1
        CONTAMINANT_ENSEMBL:ENSBTAP00000016046
        1
        4.9696
        4.9691
        4.9702
        2
        CONTAMINANT_ENSEMBL:ENSBTAP00000024146
        18
        6.4749
        6.4927
        6.4564
        3
        CONTAMINANT_ENSEMBL:ENSBTAP00000025008;sp|Q9H4B7|TBB1_HUMAN
        1
        5.3782
        5.3425
        5.4111
        4
        CONTAMINANT_ENSEMBL:ENSBTAP00000032840
        3
        5.2459
        5.2058
        5.2824
        5
        CONTAMINANT_ENSEMBL:ENSBTAP00000038329
        1
        5.3653
        5.3635
        5.3671
        6
        CONTAMINANT_O95678;sp|O95678|K2C75_HUMAN
        1
        4.8701
        4.8570
        4.8829
        7
        CONTAMINANT_P00735
        1
        4.7947
        4.8078
        4.7811
        8
        CONTAMINANT_P00761;CONTAMINANT_sp|TRYP_PIG|
        8
        6.9130
        6.9043
        6.9214
        9
        CONTAMINANT_P00978
        2
        5.4043
        5.3716
        5.4347
        10
        CONTAMINANT_P01044-1;CONTAMINANT_P01045-1;CONTAMINANT_Q2KJ62
        1
        5.1868
        5.1827
        5.1908
        11
        CONTAMINANT_P01966
        2
        5.5727
        5.6080
        5.5342
        12
        CONTAMINANT_P02584
        1
        5.2339
        5.2264
        5.2413
        13
        CONTAMINANT_P02768-1;CONTAMINANT_sp|ALBU_HUMAN|;sp|P02768|ALBU_HUMAN
        3
        6.0457
        6.0469
        6.0445
        14
        CONTAMINANT_P02769;CONTAMINANT_sp|ALBU_BOVIN|
        48
        7.2362
        7.2897
        7.1751
        15
        CONTAMINANT_P02777
        1
        5.3988
        5.3678
        5.4277
        16
        CONTAMINANT_P04264;CONTAMINANT_sp|K2C1_HUMAN|;sp|P04264|K2C1_HUMAN
        8
        5.9729
        5.9658
        5.9799
        17
        CONTAMINANT_P05787;sp|P05787-2|K2C8_HUMAN;sp|P05787|K2C8_HUMAN
        12
        6.9731
        6.9612
        6.9846
        18
        CONTAMINANT_P07477;sp|P07477|TRY1_HUMAN;sp|P07478|TRY2_HUMAN;sp|Q8NHM4|TRY6_HUMAN
        1
        5.0617
        5.0283
        5.0927
        19
        CONTAMINANT_P08727
        1
        5.1658
        5.2090
        5.1177
        20
        CONTAMINANT_P08779;sp|P08779|K1C16_HUMAN
        1
        4.9263
        5.0839
        4.6763
        21
        CONTAMINANT_P12763
        9
        6.5276
        6.5506
        6.5034
        22
        CONTAMINANT_P13645;CONTAMINANT_sp|K1C10_HUMAN|;sp|P13645|K1C10_HUMAN
        5
        5.7732
        5.7489
        5.7961
        23
        CONTAMINANT_P15497
        1
        5.5808
        5.5636
        5.5974
        24
        CONTAMINANT_P34955
        12
        6.5091
        6.5417
        6.4739
        25
        CONTAMINANT_P41361
        2
        5.3798
        5.3758
        5.3838
        26
        CONTAMINANT_Q04695;sp|Q04695|K1C17_HUMAN
        3
        5.7030
        5.6841
        5.7211
        27
        CONTAMINANT_Q0IIK2;CONTAMINANT_Q29443
        22
        6.5474
        6.5708
        6.5227
        28
        CONTAMINANT_Q1RMK2
        4
        5.4986
        5.4878
        5.5093
        29
        CONTAMINANT_Q28194;sp|P07996-2|TSP1_HUMAN;sp|P07996|TSP1_HUMAN
        4
        5.5595
        5.5490
        5.5697
        30
        CONTAMINANT_Q2M2I5;sp|Q2M2I5|K1C24_HUMAN
        1
        4.5381
        4.6007
        4.4650
        31
        CONTAMINANT_Q2UVX4
        4
        5.7020
        5.6943
        5.7097
        32
        CONTAMINANT_Q32MB2;sp|Q86Y46|K2C73_HUMAN
        1
        4.9287
        4.8952
        4.9599
        33
        CONTAMINANT_Q3KUS7
        2
        4.9367
        4.9094
        4.9625
        34
        CONTAMINANT_Q3MHN5
        2
        5.3902
        5.4161
        5.3627
        35
        CONTAMINANT_Q3SX09
        2
        5.4082
        5.4195
        5.3965
        36
        CONTAMINANT_Q3SZ57
        10
        6.1558
        6.1550
        6.1566
        37
        CONTAMINANT_Q3SZH5
        1
        4.2987
        4.2706
        4.3251
        38
        CONTAMINANT_Q3SZR3
        1
        5.0147
        4.9966
        5.0321
        39
        CONTAMINANT_Q3SZV7
        2
        5.3713
        5.3554
        5.3866
        40
        CONTAMINANT_Q3T052
        2
        5.0786
        5.0812
        5.0760
        41
        CONTAMINANT_Q3ZBD7
        2
        5.5515
        5.5718
        5.5302
        42
        CONTAMINANT_Q3ZBS7
        5
        5.9838
        6.0035
        5.9631
        43
        CONTAMINANT_Q58D62
        2
        5.1486
        5.1413
        5.1558
        44
        CONTAMINANT_Q86YZ3;sp|Q86YZ3|HORN_HUMAN
        2
        4.7705
        4.8848
        4.6148
        45
        CONTAMINANT_Q9C075;sp|Q9C075|K1C23_HUMAN
        2
        5.2826
        5.2471
        5.3155
        46
        CONTAMINANT_Q9TRI1
        3
        5.8773
        5.8820
        5.8725
        47
        CONTAMINANT_Q9TTE1
        3
        5.1829
        5.1888
        5.1769
        48
        CONTAMINANT_sp|ANXA5_HUMAN|;sp|P08758|ANXA5_HUMAN
        26
        7.0291
        7.0161
        7.0417
        49
        CONTAMINANT_sp|B2MG_HUMAN|;sp|P61769|B2MG_HUMAN
        2
        5.5923
        5.5562
        5.6257
        50
        CONTAMINANT_sp|CATA_HUMAN|;sp|P04040|CATA_HUMAN
        25
        6.9239
        6.9182
        6.9294

        nf-core/quantms Software Versions

        nf-core/quantms Software Versions are collected at run time from the software output.URL: https://github.com/nf-core/quantms

        Process Name Software Version
        CONSENSUSID ConsensusID 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        CUSTOM_DUMPSOFTWAREVERSIONS python 3.9.5
        yaml 5.4.1
        EXTRACTPSMFEATURES PSMFeatureExtractor 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        FDRCONSENSUSID FalseDiscoveryRate 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        FILEMERGE FileMerger 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        IDCONFLICTRESOLVER IDConflictResolver 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        IDFILTER IDFilter 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        IDMAPPER IDMapper 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        ISOBARICANALYZER IsobaricAnalyzer 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        MSSTATSCONVERTER MSstatsConverter 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        MSSTATSTMT bioconductor-msstatstmt 2.2.0
        r-base 4.1.1
        PERCOLATOR PercolatorAdapter 2.8.0-pre-exported-20220227 Feb 27 2022, 20:31:47
        percolator 3.05.0, Build Date Aug 31 2020 19:03:04
        PROTEININFERENCER ProteinInference 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        PROTEINQUANTIFIER ProteinQuantifier 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49
        SAMPLESHEET_CHECK sdrf-pipelines 0.0.21
        SDRFPARSING sdrf-pipelines 0.0.21
        SEARCHENGINECOMET Comet 2019.01 rev. 5
        CometAdapter 2.8.0-pre-exported-20220227 Feb 27 2022, 20:31:47
        SEARCHENGINEMSGF MSGFPlusAdapter 2.8.0-pre-exported-20220227 Feb 27 2022, 20:31:47
        msgf_plus MS-GF+ Release (v2021.03.22) (22 March 2021)
        THERMORAWFILEPARSER ThermoRawFileParser 1.3.4
        Workflow Nextflow 21.10.6
        nf-core/quantms 1.1dev

        nf-core/quantms Workflow Summary

        - this information is collected when the pipeline is started.URL: https://github.com/nf-core/quantms

        Core Nextflow options

        runName
        loving_cajal
        containerEngine
        singularity
        launchDir
        /hps/nobackup/juan/pride/reanalysis/PXD020248
        workDir
        /hps/nobackup/juan/pride/reanalysis/PXD020248/work
        projectDir
        /hps/nobackup/juan/pride/reanalysis/quantms
        userName
        pst_prd
        profile
        ebiclusters
        configFiles
        /hps/nobackup/juan/pride/reanalysis/quantms/nextflow.config, /hps/nobackup/juan/pride/reanalysis/quantms/nextflow.config

        Input/output options

        input
        PXD020248-TMT.sdrf.tsv
        outdir
        PXD020248-TMT
        root_folder
        /hps/nobackup/juan/pride/reanalysis/PXD020248/
        local_input_type
        raw

        Protein database

        database
        /hps/nobackup/juan/pride/reanalysis/multiomics-configs/databases/Homo-sapiens-uniprot-reviewed-isoforms-contaminants-decoy-202105.fasta

        Database search

        search_engines
        comet,msgf
        instrument
        N/A

        Modification localization

        luciphor_debug
        N/A

        PSM re-scoring (general)

        run_fdr_cutoff
        0.10

        PSM re-scoring (Percolator)

        description_correct_features
        N/A

        Consensus ID

        consensusid_considered_top_hits
        N/A
        min_consensus_support
        N/A

        Isobaric analyzer

        select_activation
        HCD

        Protein Quantification (DDA)

        ratios
        N/A
        normalize
        N/A
        fix_peptides
        N/A

        DIA-NN

        acquisition_method
        N/A
        mass_acc_ms2
        13
        mass_acc_ms1
        7
        scan_window
        8

        Statistical post-processing

        contrasts
        pairwise

        Quality control

        enable_pmultiqc
        true

        Max job request options

        max_cpus
        48
        max_memory
        300 GB
        max_time
        10d

        Generic options

        hostnames
        N/A